Lithium-ion secondary batteries have become key devices for energy storage for automotive and renewable energy applications. To further improve battery performance, clarification of the ion transport phenomena within the batteries is necessary. However, experimental investigation has not yet been performed. In this study, in situ visualization of lithium-ion batteries with a hard carbon or graphite negative electrode was achieved using low-energy X-ray microscopy. Visualization experiments were conducted on two different negative electrode materials. The concentration distributions of lithium ions (Li⁺) and hexafluorophosphate ions (PF₆⁻) inside the hard carbon negative electrode were investigated. Additionally, stage transformation caused by lithium intercalation was observed in the graphite negative electrode. These results suggest that transport phenomena in the electrodes of operating lithium-ion batteries can be investigated using low-energy X-ray microscopy.